tree_subset {treeio} | R Documentation |
This function allows for a tree object to be subset by specifying a node and returns all related nodes within a selected number of levels
tree_subset(tree, node, levels_back = 5, group_node = TRUE, group_name = "group", root_edge = TRUE) ## S3 method for class 'phylo' tree_subset(tree, node, levels_back = 5, group_node = TRUE, group_name = "group", root_edge = TRUE) ## S3 method for class 'treedata' tree_subset(tree, node, levels_back = 5, group_node = TRUE, group_name = "group", root_edge = TRUE)
tree |
a tree object of class phylo |
node |
either a tip label or a node number for the given tree that will be the focus of the subsetted tree |
levels_back |
a number specifying how many nodes back from the selected node the subsetted tree should include |
group_node |
whether add grouping information of selected node |
group_name |
group name (default 'group') for storing grouping information if group_node = TRUE |
root_edge |
If TRUE (by default), set root.edge to path length of orginal root to the root of subset tree |
This function will take a tree and a specified node from
that tree and subset the tree showing all relatives back to a specified
number of nodes. This function allows for a combination of
ancestor
and offspring
to return a subsetted
tree that is of class phylo. This allows for easy graphing of the tree
with ggtree
## Not run: nwk <- system.file("extdata", "sample.nwk", package="treeio") tree <- read.tree(nwk) sub_tree <- tree_subset(tree, node = "A", levels_back = 3) ggtree(sub_tree) + geom_tiplab() + geom_nodelab() ## End(Not run) ## Not run: nwk <- system.file("extdata", "sample.nwk", package="treeio") tree <- read.tree(nwk) sub_tree <- tree_subset(tree, node = "A", levels_back = 3) ggtree(sub_tree) + geom_tiplab() + geom_nodelab() ## End(Not run)